Clean Installer is a handy tool for finding duplicate files and getting rid of them.
Just wrote a lengthy reply which includes data about Clean Installer, so just going to copy/paste the relevant part again here:
If you don't already have it, download and install Clean Installer:
http://sims2pack.modthesims2.com/index.php?page=1Run Clean Installer and let it scan your Downloads file and finish generating the list of files.
Then click the MD5 tab in Clean Installer - this will group files so you can find duplicates more easily.
As you scroll down the list, look for items highlighted in pink - those are duplicates. Remove them all but one from each group.
Then click the Type tab in Clean Installer, and scroll down the type column to the 'E' section, and see if there are any files listed as "Empty Package.' Delete any listed as Empty Package.
Note: Clean Installer also highlights any hacks in red. This is not a danger sign, just a highlighting. Don't delete the red items, unless you don't want the hacks. Custom lots, especially, can come with included hacks which you may not want or which may be incompatible with your version of the game.
Be aware that if you Remove a file using Clean Installer - it is gone - there is no Undo to get it back.
As for the Thumbnails, you can try this:
Open your My Documents--EA Games--The Sims 2--Thumbnails folder.
Delete everything in the folder (but not the folder itself).
The game will generate all new thumbnails for you as you access any part of the game which uses thumbnails (things may run a bit slower than normal the first time only, as the new thumbnails are generated).
As someone above mentioned, you can also use Delphy's Organizer, but it can and does also give false positives, so bear that in mind when using it.